1
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Ahmed MMA, Boudreau PD. LCMS-Metabolomic Profiling and Genome Mining of Delftia lacustris DSM 21246 Revealed Lipophilic Delftibactin Metallophores. J Nat Prod 2024. [PMID: 38739531 DOI: 10.1021/acs.jnatprod.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Bacteria have evolved various strategies to combat heavy metal stress, including the secretion of small molecules, known as metallophores. These molecules hold a potential role in the mitigation of toxic metal contamination from the environment (bioremediation). Herein, we employed combined comparative metabolomic and genomic analyses to study the metallophores excreted by Delftia lacustris DSM 21246. LCMS-metabolomic analysis of this bacterium cultured under iron limitation led to a suite of lipophilic metallophores exclusively secreted in response to iron starvation. Additionally, we conducted genome sequencing of the DSM 21246 strain using nanopore sequencing technology and employed antiSMASH to mine the genome, leading to the identification of a biosynthetic gene cluster (BGC) matching the known BGC responsible for delftibactin A production. The isolated suite of amphiphilic metallophores, termed delftibactins C-F (1-4), was characterized using various chromatographic, spectroscopic, and bioinformatic techniques. The planar structure of these compounds was elucidated through 1D and 2D NMR analyses, as well as LCMS/MS-based fragmentation studies. Notably, their structures differed from previously known delftibactins due to the presence of a lipid tail. Marfey's and bioinformatic analyses were employed to determine the absolute configuration of the peptide scaffold. Delftibactin A, a previously identified metallophore, has exhibited a gold biomineralizing property; compound 1 was tested for and also demonstrated this property.
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Affiliation(s)
- Mohammed M A Ahmed
- Boudreau Lab, Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
- Department of Pharmacognosy, Al-Azhar University, Cairo 11651, Egypt
| | - Paul D Boudreau
- Boudreau Lab, Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
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2
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Ngo TE, Ecker A, Ryu B, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Thomas L, Dahesh S, Nizet V, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from Marine Cyanobacterium Moorena producens JHB Discovered via Coculture with Candida albicans. ACS Chem Biol 2024; 19:619-628. [PMID: 38330248 PMCID: PMC10949194 DOI: 10.1021/acschembio.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies on this strain led to the discovery of several novel compounds such as hectochlorins and jamaicamides. However, bioinformatic analyses of its genome indicate the presence of numerous cryptic biosynthetic gene clusters that have yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was cocultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that coculture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrew Ecker
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Byeol Ryu
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Aurora Guild
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ariana Remmel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul D. Boudreau
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of BioMolecular Sciences,University of Mississippi,
School of Pharmacy, University, Mississippi 38677, United States
| | - Kelsey L. Alexander
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Chemistry, University of California San
Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - C. Benjamin Naman
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Science and Conservation, San Diego Botanic
Garden, 300 Quail Gardens
Drive, Encinitas, California 92024, United States
| | - Evgenia Glukhov
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nicole E. Avalon
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vikram V. Shende
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lamar Thomas
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Samira Dahesh
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Victor Nizet
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lena Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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3
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Ahmed MMA, Tripathi SK, Boudreau PD. Comparative metabolomic profiling of Cupriavidus necator B-4383 revealed production of cupriachelin siderophores, one with activity against Cryptococcus neoformans. Front Chem 2023; 11:1256962. [PMID: 37693169 PMCID: PMC10484230 DOI: 10.3389/fchem.2023.1256962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Cupriavidus necator H16 is known to be a rich source of linear lipopeptide siderophores when grown under iron-depleted conditions; prior literature termed these compounds cupriachelins. These small molecules bear β-hydroxyaspartate moieties that contribute to a photoreduction of iron when bound as ferric cupriachelin. Here, we present structural assignment of cupriachelins from C. necator B-4383 grown under iron limitation. The characterization of B-4383 cupriachelins is based on MS/MS fragmentation analysis, which was confirmed by 1D- and 2D-NMR for the most abundant analog (1). The cupriachelin congeners distinguish these two strains with differences in the preferred lipid tail; however, our rigorous metabolomic investigation also revealed minor analogs with changes in the peptide core, hinting at a potential mechanism by which these siderophores may reduce biologically unavailable ferric iron (4-6). Antifungal screening of the C. necator B-4383 supernatant extract and the isolated cupriachelin analog (1) revealed inhibitory activity against Cryptococcus neoformans, with IC50 values of 16.6 and 3.2 μg/mL, respectively. This antifungal activity could be explained by the critical role of the iron acquisition pathway in the growth and pathogenesis of the C. neoformans fungal pathogen.
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Affiliation(s)
- Mohammed M. A. Ahmed
- Boudreau Lab, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
- Department of Pharmacognosy, Al-Azhar University, Cairo, Egypt
| | - Siddarth K. Tripathi
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Paul D. Boudreau
- Boudreau Lab, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
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4
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Ngo TE, Ecker A, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from the Marine Cyanobacterium Moorena producens JHB Discovered via Co-culture with Candida albicans. bioRxiv 2023:2023.07.06.547815. [PMID: 37461655 PMCID: PMC10350029 DOI: 10.1101/2023.07.06.547815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies of this strain led to the discovery of several novel compounds such as the hectochlorins and jamaicamides; however, bioinformatic analyses of its genome suggested that there were many more cryptic biosynthetic gene clusters yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was co-cultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that co-culture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrew Ecker
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Aurora Guild
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ariana Remmel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of BioMolecular Sciences, University of Mississippi School of Pharmacy, University, Mississippi 38677, USA
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Science and Conservation, San Diego Botanic Garden, 300 Quail Gardens Drive, Encinitas, CA, 92024, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nicole E Avalon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vikram V Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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5
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Kim GJ, Mascuch SJ, Mevers E, Boudreau PD, Gerwick WH, Choi H. Luquilloamides, Cytotoxic Lipopeptides from a Puerto Rican Collection of the Filamentous Marine Cyanobacterium Oscillatoria sp. J Org Chem 2021; 87:1043-1055. [PMID: 34967649 DOI: 10.1021/acs.joc.1c02340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Luquilloamides A-G (1-7) were isolated from a small environmental collection of a marine cyanobacterium found growing on eelgrass (Zostera sp.) near Luquillo, Puerto Rico. Structure elucidation of the luquilloamides was accomplished via detailed NMR and MS analyses, and absolute configurations were determined using a combination of advanced Mosher's method, J-based configuration analysis, semisynthetic fragment analysis derived from ozonolysis, methylation, Baeyer-Villiger oxidation, Mosher's esterification, specific rotations, and ECD data. Except for 2, the luquilloamides share a characteristic tert-butyl-containing polyketide fragment, β-alanine, and a proposed highly modified polyketide extension. While compound 1 is a linear lipopeptide with two α-methyl branches and a vinyl chloride functionality in the polyketide portion, compounds 4, 6, and 7 possess a cyclohexanone structure with methylation on the α- or β-positions of the polyketide as well as an acetyl group. Interestingly, the absolute configuration at C-5 and C-6 on the cyclohexanone unit in 7 is opposite to that of 4-6. Compound 3 was revealed to have a tert-butyl-containing polyketide, β-alanine, and a PKS/NRPS-derived γ-isopropyl pyrrolinone. Compound 2 may be a hydrolysis product of 3. Of the seven new compounds, 1 showed the most potent cytotoxicity to human H-460 lung cancer cells.
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Affiliation(s)
- Geum Jin Kim
- College of Pharmacy and Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Emily Mevers
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States.,Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States.,Department of BioMolecular Sciences, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Hyukjae Choi
- College of Pharmacy and Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
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6
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Boudreau PD, Miller BW, McCall LI, Almaliti J, Reher R, Hirata K, Le T, Siqueira-Neto JL, Hook V, Gerwick WH. Design of Gallinamide A Analogs as Potent Inhibitors of the Cysteine Proteases Human Cathepsin L and Trypanosoma cruzi Cruzain. J Med Chem 2019; 62:9026-9044. [PMID: 31539239 DOI: 10.1021/acs.jmedchem.9b00294] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Gallinamide A, originally isolated with a modest antimalarial activity, was subsequently reisolated and characterized as a potent, selective, and irreversible inhibitor of the human cysteine protease cathepsin L. Molecular docking identified potential modifications to improve binding, which were synthesized as a suite of analogs. Resultingly, this current study produced the most potent gallinamide analog yet tested against cathepsin L (10, Ki = 0.0937 ± 0.01 nM and kinact/Ki = 8 730 000). From a protein structure and substrate preference perspective, cruzain, an essential Trypanosoma cruzi cysteine protease, is highly homologous. Our investigations revealed that gallinamide and its analogs potently inhibit cruzain and are exquisitely toxic toward T. cruzi in the intracellular amastigote stage. The most active compound, 5, had an IC50 = 5.1 ± 1.4 nM, but was relatively inactive to both the epimastigote (insect stage) and the host cell, and thus represents a new candidate for the treatment of Chagas disease.
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Affiliation(s)
| | | | | | - Jehad Almaliti
- Department of Pharmaceutical Sciences, College of Pharmacy , The University of Jordan , Amman 11942 , Jordan
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7
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Wilson MR, Jiang Y, Villalta PW, Stornetta A, Boudreau PD, Carrá A, Brennan CA, Chun E, Ngo L, Samson LD, Engelward BP, Garrett WS, Balbo S, Balskus EP. The human gut bacterial genotoxin colibactin alkylates DNA. Science 2019; 363:363/6428/eaar7785. [PMID: 30765538 DOI: 10.1126/science.aar7785] [Citation(s) in RCA: 322] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/16/2018] [Accepted: 12/21/2018] [Indexed: 12/13/2022]
Abstract
Certain Escherichia coli strains residing in the human gut produce colibactin, a small-molecule genotoxin implicated in colorectal cancer pathogenesis. However, colibactin's chemical structure and the molecular mechanism underlying its genotoxic effects have remained unknown for more than a decade. Here we combine an untargeted DNA adductomics approach with chemical synthesis to identify and characterize a covalent DNA modification from human cell lines treated with colibactin-producing E. coli Our data establish that colibactin alkylates DNA with an unusual electrophilic cyclopropane. We show that this metabolite is formed in mice colonized by colibactin-producing E. coli and is likely derived from an initially formed, unstable colibactin-DNA adduct. Our findings reveal a potential biomarker for colibactin exposure and provide mechanistic insights into how a gut microbe may contribute to colorectal carcinogenesis.
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Affiliation(s)
- Matthew R Wilson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Paul D Boudreau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Andrea Carrá
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Caitlin A Brennan
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lizzie Ngo
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Institute, Boston, MA 02115, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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8
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Jiang Y, Stornetta A, Villalta PW, Wilson MR, Boudreau PD, Zha L, Balbo S, Balskus EP. Reactivity of an Unusual Amidase May Explain Colibactin's DNA Cross-Linking Activity. J Am Chem Soc 2019; 141:11489-11496. [PMID: 31251062 PMCID: PMC6728428 DOI: 10.1021/jacs.9b02453] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Certain commensal and pathogenic bacteria produce colibactin, a small-molecule genotoxin that causes interstrand cross-links in host cell DNA. Although colibactin alkylates DNA, the molecular basis for cross-link formation is unclear. Here, we report that the colibactin biosynthetic enzyme ClbL is an amide bond-forming enzyme that links aminoketone and β-keto thioester substrates in vitro and in vivo. The substrate specificity of ClbL strongly supports a role for this enzyme in terminating the colibactin NRPS-PKS assembly line and incorporating two electrophilic cyclopropane warheads into the final natural product scaffold. This proposed transformation was supported by the detection of a colibactin-derived cross-linked DNA adduct. Overall, this work provides a biosynthetic explanation for colibactin's DNA cross-linking activity and paves the way for further study of its chemical structure and biological roles.
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Affiliation(s)
- Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, United States
| | - Peter W. Villalta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, United States
| | - Matthew R. Wilson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Paul D. Boudreau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Li Zha
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
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9
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Mascuch SJ, Boudreau PD, Carland TM, Pierce NT, Olson J, Hensler ME, Choi H, Campanale J, Hamdoun A, Nizet V, Gerwick WH, Gaasterland T, Gerwick L. Marine Natural Product Honaucin A Attenuates Inflammation by Activating the Nrf2-ARE Pathway. J Nat Prod 2018; 81:506-514. [PMID: 29215273 PMCID: PMC6553616 DOI: 10.1021/acs.jnatprod.7b00734] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The cyanobacterial marine natural product honaucin A inhibits mammalian innate inflammation in vitro and in vivo. To decipher its mechanism of action, RNA sequencing was used to evaluate differences in gene expression of cultured macrophages following honaucin A treatment. This analysis led to the hypothesis that honaucin A exerts its anti-inflammatory activity through activation of the cytoprotective nuclear erythroid 2-related factor 2 (Nrf2)-antioxidant response element/electrophile response element (ARE/EpRE) signaling pathway. Activation of this pathway by honaucin A in cultured human MCF7 cells was confirmed using an Nrf2 luciferase reporter assay. In vitro alkylation experiments with the natural product and N-acetyl-l-cysteine suggest that honaucin A activates this pathway through covalent interaction with the sulfhydryl residues of the cytosolic repressor protein Keap1. Honaucin A presents a potential therapeutic lead for diseases with an inflammatory component modulated by Nrf2-ARE.
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Affiliation(s)
- Samantha J. Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | | | - N. Tessa Pierce
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Joshua Olson
- Department of Pediatrics, School of Medicine, and University of California, San Diego, La Jolla, California 92093, United States University of California, San Diego, La Jolla, California 92093, United States
| | - Mary E. Hensler
- Department of Pediatrics, School of Medicine, and University of California, San Diego, La Jolla, California 92093, United States University of California, San Diego, La Jolla, California 92093, United States
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Joseph Campanale
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, and University of California, San Diego, La Jolla, California 92093, United States University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Teresa Gaasterland
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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10
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2017; 34:828-837. [PMID: 27504778 DOI: 10.1038/nbt.3597] [Citation(s) in RCA: 2254] [Impact Index Per Article: 322.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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11
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Naman CB, Rattan R, Nikoulina SE, Lee J, Miller BW, Moss NA, Armstrong L, Boudreau PD, Debonsi HM, Valeriote FA, Dorrestein PC, Gerwick WH. Integrating Molecular Networking and Biological Assays To Target the Isolation of a Cytotoxic Cyclic Octapeptide, Samoamide A, from an American Samoan Marine Cyanobacterium. J Nat Prod 2017; 80:625-633. [PMID: 28055219 PMCID: PMC5758054 DOI: 10.1021/acs.jnatprod.6b00907] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Integrating LC-MS/MS molecular networking and bioassay-guided fractionation enabled the targeted isolation of a new and bioactive cyclic octapeptide, samoamide A (1), from a sample of cf. Symploca sp. collected in American Samoa. The structure of 1 was established by detailed 1D and 2D NMR experiments, HRESIMS data, and chemical degradation/chromatographic (e.g., Marfey's analysis) studies. Pure compound 1 was shown to have in vitro cytotoxic activity against several human cancer cell lines in both traditional cell culture and zone inhibition bioassays. Although there was no particular selectivity between the cell lines tested for samoamide A, the most potent activity was observed against H460 human non-small-cell lung cancer cells (IC50 = 1.1 μM). Molecular modeling studies suggested that one possible mechanism of action for 1 is the inhibition of the enzyme dipeptidyl peptidase (CD26, DPP4) at a reported allosteric binding site, which could lead to many downstream pharmacological effects. However, this interaction was moderate when tested in vitro at up to 10 μM and only resulted in about 16% peptidase inhibition. Combining bioassay screening with the cheminformatics strategy of LC-MS/MS molecular networking as a discovery tool expedited the targeted isolation of a natural product possessing both a novel chemical structure and a desired biological activity.
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Affiliation(s)
- C. Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Ramandeep Rattan
- Division of Gynecology Oncology, Department of Women’s Health Services, Henry Ford Hospital, Detroit, Michigan 48202, United States
| | - Svetlana E. Nikoulina
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - John Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Bailey W. Miller
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Nathan A. Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Lorene Armstrong
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Hosana M. Debonsi
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Frederick A. Valeriote
- Division of Hematology and Oncology, Department of Internal Medicine, Henry Ford Hospital, Detroit, Michigan 48202, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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12
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016. [PMID: 27504778 DOI: 10.1038/nbt.3597.sharing] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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13
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Willumstad TP, Boudreau PD, Danheiser RL. Synthesis of Highly Substituted Quinolines via a Tandem Ynamide Benzannulation/Iodocyclization Strategy. J Org Chem 2015; 80:11794-805. [PMID: 26259034 DOI: 10.1021/acs.joc.5b01648] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A two-stage "tandem strategy" for the regiocontrolled synthesis of very highly substituted quinolines is described. Benzannulation based on the reaction of cyclobutenones or diazo ketones with N-propargyl-substituted ynamides proceeds via a cascade of several pericyclic reactions to generate multiply substituted aniline derivatives. In the second stage of the tandem strategy, triflate derivatives of the phenolic benzannulation products undergo Larock cyclization upon exposure to iodine to form products that are further elaborated by methods such as palladium-catalyzed coupling to generate quinolines that can be substituted at every position of the bicyclic system.
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Affiliation(s)
- Thomas P Willumstad
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139, United States
| | - Paul D Boudreau
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139, United States
| | - Rick L Danheiser
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139, United States
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14
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Boudreau PD, Monroe EA, Mehrotra S, Desfor S, Korobeynikov A, Sherman DH, Murray TF, Gerwick L, Dorrestein PC, Gerwick WH. Expanding the Described Metabolome of the Marine Cyanobacterium Moorea producens JHB through Orthogonal Natural Products Workflows. PLoS One 2015. [PMID: 26222584 PMCID: PMC4519256 DOI: 10.1371/journal.pone.0133297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Moorea producens JHB, a Jamaican strain of tropical filamentous marine cyanobacteria, has been extensively studied by traditional natural products techniques. These previous bioassay and structure guided isolations led to the discovery of two exciting classes of natural products, hectochlorin (1) and jamaicamides A (2) and B (3). In the current study, mass spectrometry-based 'molecular networking' was used to visualize the metabolome of Moorea producens JHB, and both guided and enhanced the isolation workflow, revealing additional metabolites in these compound classes. Further, we developed additional insight into the metabolic capabilities of this strain by genome sequencing analysis, which subsequently led to the isolation of a compound unrelated to the jamaicamide and hectochlorin families. Another approach involved stimulation of the biosynthesis of a minor jamaicamide metabolite by cultivation in modified media, and provided insights about the underlying biosynthetic machinery as well as preliminary structure-activity information within this structure class. This study demonstrated that these orthogonal approaches are complementary and enrich secondary metabolomic coverage even in an extensively studied bacterial strain.
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Affiliation(s)
- Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, United States
| | - Emily A. Monroe
- Department of Biology, William Paterson University, Wayne, New Jersey, 07470, United States of America
| | - Suneet Mehrotra
- Department of Pharmacology, Creighton University School of Medicine, Omaha, Nebraska, 68178, United States of America
| | - Shane Desfor
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, United States
- Department of Biology, California State University San Marcos, San Marcos, California, 92078, United States of America
| | - Anton Korobeynikov
- Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, 194021, Russia
- Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, 194021, Russia
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, 194021, Russia
| | - David H. Sherman
- Life Sciences Institute and Department of Medical Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States of America
| | - Thomas F. Murray
- Department of Pharmacology, Creighton University School of Medicine, Omaha, Nebraska, 68178, United States of America
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, United States
| | - Pieter C. Dorrestein
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92093, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093, United States of America
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093, United States of America
- * E-mail:
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15
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Moree WJ, McConnell OJ, Nguyen DD, Sanchez LM, Yang YL, Zhao X, Liu WT, Boudreau PD, Srinivasan J, Atencio L, Ballesteros J, Gavilán RG, Torres-Mendoza D, Guzmán HM, Gerwick WH, Gutiérrez M, Dorrestein PC. Microbiota of healthy corals are active against fungi in a light-dependent manner. ACS Chem Biol 2014; 9:2300-8. [PMID: 25058318 PMCID: PMC4201335 DOI: 10.1021/cb500432j] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Coral
reefs are intricate ecosystems that harbor diverse organisms,
including 25% of all marine fish. Healthy corals exhibit a complex
symbiosis between coral polyps, endosymbiotic alga, and an array of
microorganisms, called the coral holobiont. Secretion of specialized
metabolites by coral microbiota is thought to contribute to the defense
of this sessile organism against harmful biotic and abiotic factors.
While few causative agents of coral diseases have been unequivocally
identified, fungi have been implicated in the massive destruction
of some soft corals worldwide. Because corals are nocturnal feeders,
they may be more vulnerable to fungal infection at night, and we hypothesized
that the coral microbiota would have the capability to enhance their
defenses against fungi in the dark. A Pseudoalteromonas sp. isolated from a healthy octocoral displayed light-dependent
antifungal properties when grown adjacent to Penicilliumcitrinum (P. citrinum) isolated
from a diseased Gorgonian octocoral. Microbial MALDI-imaging mass
spectrometry (IMS) coupled with molecular network analyses revealed
that Pseudoalteromonas produced higher levels of
antifungal polyketide alteramides in the dark than in the light. The
alteramides were inactivated by light through a photoinduced intramolecular
cyclization. Further NMR studies led to a revision of the stereochemical
structure of the alteramides. Alteramide A exhibited antifungal properties
and elicited changes in fungal metabolite distributions of mycotoxin
citrinin and citrinadins. These data support the hypothesis that coral
microbiota use abiotic factors such as light to regulate the production
of metabolites with specialized functions to combat opportunistic
pathogens at night.
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Affiliation(s)
| | | | | | | | - Yu-Liang Yang
- Agricultural
Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | | | | | - Librada Atencio
- Instituto de Investigaciones
Científicas y Servicios de Alta Tecnología (INDICASAT),
Ciudad del Saber, Clayton 0843-01103, Panamá
| | - Javier Ballesteros
- Instituto de Investigaciones
Científicas y Servicios de Alta Tecnología (INDICASAT),
Ciudad del Saber, Clayton 0843-01103, Panamá
| | - Ronnie G. Gavilán
- Instituto de Investigaciones
Científicas y Servicios de Alta Tecnología (INDICASAT),
Ciudad del Saber, Clayton 0843-01103, Panamá
- National Center for Public Health, National Institute of Health, Capac Yupanqui 1400 - Jesus Maria, Lima 11, Peru
| | - Daniel Torres-Mendoza
- Instituto de Investigaciones
Científicas y Servicios de Alta Tecnología (INDICASAT),
Ciudad del Saber, Clayton 0843-01103, Panamá
| | - Héctor M. Guzmán
- Smithsonian Tropical Research Institute, P.O. Box
0843-03092, Balboa, Ancón, Panamá
| | | | - Marcelino Gutiérrez
- Instituto de Investigaciones
Científicas y Servicios de Alta Tecnología (INDICASAT),
Ciudad del Saber, Clayton 0843-01103, Panamá
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16
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Mevers E, Haeckl FPJ, Boudreau PD, Byrum T, Dorrestein PC, Valeriote F, Gerwick WH. Lipopeptides from the tropical marine cyanobacterium Symploca sp. J Nat Prod 2014; 77:969-975. [PMID: 24588245 PMCID: PMC4002153 DOI: 10.1021/np401051z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 06/02/2023]
Abstract
A collection of the tropical marine cyanobacterium Symploca sp., collected near Kimbe Bay, Papua New Guinea, previously yielded several new metabolites including kimbeamides A-C, kimbelactone A, and tasihalide C. Investigations into a more polar cytotoxic fraction yielded three new lipopeptides, tasiamides C-E (1-3). The planar structures were deduced by 2D NMR spectroscopy and tandem mass spectrometry, and their absolute configurations were determined by a combination of Marfey's and chiral-phase GC-MS analysis. These new metabolites are similar to several previously isolated compounds, including tasiamide (4), grassystatins (5, 6), and symplocin A, all of which were isolated from similar filamentous marine cyanobacteria.
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Affiliation(s)
- Emily Mevers
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - F. P. Jake Haeckl
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Paul D. Boudreau
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Tara Byrum
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Frederick
A. Valeriote
- Division
of Hematology and Oncology, Department of Internal Medicine, Henry Ford Hospital, Detroit, Michigan 48202, United States
| | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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17
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Liu WT, Lamsa A, Wong WR, Boudreau PD, Kersten R, Peng Y, Moree WJ, Duggan BM, Moore BS, Gerwick WH, Linington RG, Pogliano K, Dorrestein PC. MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus. J Antibiot (Tokyo) 2013; 67:99-104. [PMID: 24149839 DOI: 10.1038/ja.2013.99] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/24/2013] [Accepted: 07/27/2013] [Indexed: 02/06/2023]
Abstract
Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the 'molecular network' of that organism, followed by studies to characterize the cellular effects of antibacterial molecules. We demonstrate that Streptomyces roseosporus produces at least four non-ribosomal peptide synthetase-derived molecular families and their gene subnetworks (daptomycin, arylomycin, napsamycin and stenothricin) were identified with different modes of action. A number of previously unreported analogs involving truncation, glycosylation, hydrolysis and biosynthetic intermediates and/or shunt products were also captured and visualized by creation of a map through MS/MS networking. The diversity of antibacterial compounds produced by S. roseosporus highlights the importance of developing new approaches to characterize the molecular capacity of an organism in a more global manner. This allows one to more deeply interrogate the biosynthetic capacities of microorganisms with the goal to streamline the discovery pipeline for biotechnological applications in agriculture and medicine. This is a contribution to a special issue to honor Chris Walsh's amazing career.
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Affiliation(s)
- Wei-Ting Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Anne Lamsa
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Weng Ruh Wong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Roland Kersten
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Yao Peng
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wilna J Moree
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Brendan M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- 1] Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA [2] Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA [3] Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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18
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Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Ruh Wong W, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. Molecular networking as a dereplication strategy. J Nat Prod 2013; 76:1686-99. [PMID: 24025162 PMCID: PMC3936340 DOI: 10.1021/np400413s] [Citation(s) in RCA: 400] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.
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Affiliation(s)
- Jane Y. Yang
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Laura M. Sanchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Christopher M. Rath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Xueting Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100190, China
| | - Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Nicole Bruns
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Anne Wodtke
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Rafael de Felicio
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Nucleo de Pesquisaem Produtos Naturais e Sinteticos - Departamento de Fisica e Quimica - Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - Amanda Fenner
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Weng Ruh Wong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Lixin Zhang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100190, China
| | - Hosana M. Debonsi
- Nucleo de Pesquisaem Produtos Naturais e Sinteticos - Departamento de Fisica e Quimica - Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Corresponding Author Telephone: 858-534-6607 Fax: 858-822-0041
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Boudreau PD, Byrum T, Liu WT, Dorrestein PC, Gerwick WH. Viequeamide A, a cytotoxic member of the kulolide superfamily of cyclic depsipeptides from a marine button cyanobacterium. J Nat Prod 2012; 75:1560-70. [PMID: 22924493 PMCID: PMC3521035 DOI: 10.1021/np300321b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The viequeamides, a family of 2,2-dimethyl-3-hydroxy-7-octynoic acid (Dhoya)-containing cyclic depsipeptides, were isolated from a shallow subtidal collection of a "button" cyanobacterium (Rivularia sp.) from near the island of Vieques, Puerto Rico. Planar structures of the two major compounds, viequeamide A (1) and viequeamide B (2), were elucidated by 2D-NMR spectroscopy and mass spectrometry, whereas absolute configurations were determined by traditional hydrolysis, derivative formation, and chromatography in comparison with standards. In addition, a series of related minor metabolites, viequeamides C-F (3-6), were characterized by HRMS fragmentation methods. Viequeamide A was found to be highly toxic to H460 human lung cancer cells (IC(50) = 60 ± 10 nM), whereas the mixture of B-F was inactive. From a broader perspective, the viequeamides help to define a "superfamily" of related cyanobacterial natural products, the first of which to be discovered was kulolide. Within the kulolide superfamily, a wide variation in biological properties is observed, and the reported producing strains are also highly divergent, giving rise to several intriguing questions about structure-activity relationships and the evolutionary origins of this metabolite class.
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Affiliation(s)
- Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Tara Byrum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Wei-Ting Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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